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0  structures 255  species 0  interactions 449  sequences 15  architectures

Family: TRAPPC9-Trs120 (PF08626)

Summary: Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

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Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit Provide feedback

This region is found at the N terminal of Saccharomyces cerevisiae Trs120 protein (Q04183). Trs120 is a subunit of the multiprotein complex TRAPP (transport particle protein) which functions in ER to Golgi traffic [1]. Trs120 is specific to the larger TRAPP complex, TRAPP II, along with Trs65p and Trs130p(TRAPPC10). It is suggested that Trs120p is required for the stability of the Trs130p subunit, suggesting that these two proteins might interact in some way [2]. It is likely that there is a complex function for TRAPP II in multiple pathways [3].

Literature references

  1. Sacher M, Barrowman J, Schieltz D, Yates JR 3rd, Ferro-Novick S; , Eur J Cell Biol. 2000;79:71-80.: Identification and characterization of five new subunits of TRAPP. PUBMED:10727015 EPMC:10727015

  2. Morozova N, Liang Y, Tokarev AA, Chen SH, Cox R, Andrejic J, Lipatova Z, Sciorra VA, Emr SD, Segev N;, Nat Cell Biol. 2006;8:1263-1269.: TRAPPII subunits are required for the specificity switch of a Ypt-Rab GEF. PUBMED:17041589 EPMC:17041589

  3. Sacher M, Kim YG, Lavie A, Oh BH, Segev N;, Traffic. 2008;9:2032-2042.: The TRAPP complex: insights into its architecture and function. PUBMED:18801063 EPMC:18801063


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013935

The trafficking protein particle complex TRAPP is a multi-protein complex needed in the early stages of the secretory pathway. To date, two kinds of TRAPP complexes have been studied, TRAPPI and TRAPP II. These complexes differ in subunit composition [PUBMED:11239471]. TRAPP I binds vesicles derived from the endoplasmic reticulum bringing them closer to the acceptor membrane. Trs120 is a subunit specific to the TRAPP II complex [PUBMED:10727015] along with Trs65p and Trs130p(TRAPPC10). It is suggested that Trs120p is required for the stability of the Trs130p subunit, suggesting that these two proteins might interact in some way [PUBMED:17041589]. It is likely that there is a complex function for TRAPP II in multiple pathways [PUBMED:18801063].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan SNARE (CL0212), which has the following description:

This clan includes part of the SNARE like superfamily.

The clan contains the following 7 members:

Clat_adaptor_s Gryzun Gryzun-like Sedlin_N Sybindin TRAPPC10 TRAPPC9-Trs120

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(9)
Full
(449)
Representative proteomes NCBI
(471)
Meta
(2)
RP15
(116)
RP35
(199)
RP55
(276)
RP75
(329)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(9)
Full
(449)
Representative proteomes NCBI
(471)
Meta
(2)
RP15
(116)
RP35
(199)
RP55
(276)
RP75
(329)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(9)
Full
(449)
Representative proteomes NCBI
(471)
Meta
(2)
RP15
(116)
RP35
(199)
RP55
(276)
RP75
(329)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_15686 (release 19.0)
Previous IDs: Trs120;
Type: Family
Author: Mistry J, Wood V
Number in seed: 9
Number in full: 449
Average length of the domain: 725.10 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 78.18 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.3 19.3
Trusted cut-off 19.4 20.0
Noise cut-off 19.1 19.2
Model length: 1185
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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